Enable STRs in v4 (#1305)

broadinstitute · Nov 17, 2023 · d9085aa · d9085aa
1 parent e148e22
commit d9085aa
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Showing 6 changed files with 23 additions and 18 deletions.
diff --git a/browser/src/HomePage.tsx b/browser/src/HomePage.tsx
@@ -156,16 +156,21 @@ export default () => (
       </ListItem>
       {/* @ts-expect-error TS(2746) FIXME: This JSX tag's 'children' prop expects a single ch... Remove this comment to see the full error message */}
       <ListItem>
-        {/* @ts-expect-error TS(2786) FIXME: 'ExternalLink' cannot be used as a JSX component. */}
-        <ExternalLink href="https://gnomad.broadinstitute.org/short-tandem-repeats?dataset=gnomad_r3">
-          Short tandem repeat
-        </ExternalLink>{' '}
+        <Link
+          preserveSelectedDataset={false}
+          to={{
+            pathname: '/short-tandem-repeats',
+            search: queryString.stringify({ dataset: 'gnomad_r4' }),
+          }}
+        >
+          Short tandem repeat{' '}
+        </Link>
         locus:{' '}
         <Link
           preserveSelectedDataset={false}
           to={{
             pathname: 'short-tandem-repeat/ATXN1',
-            search: queryString.stringify({ dataset: 'gnomad_r3' }),
+            search: queryString.stringify({ dataset: 'gnomad_r4' }),
           }}
         >
           ATXN1

diff --git a/browser/src/RegionPage/__snapshots__/RegionPageContainer.spec.tsx.snap b/browser/src/RegionPage/__snapshots__/RegionPageContainer.spec.tsx.snap
@@ -772,7 +772,7 @@ exports[`RegionPageContainer with dataset gnomad_r4 queries API with correct par
   variables={
     {
       "chrom": "12",
-      "includeShortTandemRepeats": false,
+      "includeShortTandemRepeats": true,
       "referenceGenome": "GRCh38",
       "shortTandemRepeatDatasetId": "gnomad_r3",
       "start": 345,

diff --git a/browser/src/ShortTandemRepeatsPage/ShortTandemRepeatsPage.tsx b/browser/src/ShortTandemRepeatsPage/ShortTandemRepeatsPage.tsx
@@ -2,7 +2,7 @@ import React from 'react'
 
 import { BaseTable, ExternalLink, Page } from '@gnomad/ui'
 
-import { DatasetId, labelForDataset } from '@gnomad/dataset-metadata/metadata'
+import { DatasetId, hasShortTandemRepeats, labelForDataset } from '@gnomad/dataset-metadata/metadata'
 import DocumentTitle from '../DocumentTitle'
 import GnomadPageHeading from '../GnomadPageHeading'
 import Link from '../Link'
@@ -133,7 +133,7 @@ const ShortTandemRepeatsPageContainer = ({ datasetId }: ShortTandemRepeatsPageCo
       >
         Pathogenic Short Tandem Repeats
       </GnomadPageHeading>
-      {datasetId === 'gnomad_r3' ? (
+      {hasShortTandemRepeats(datasetId) ? (
         <Query
           operationName={operationName}
           query={query}

diff --git a/browser/src/__snapshots__/HomePage.spec.tsx.snap b/browser/src/__snapshots__/HomePage.spec.tsx.snap
@@ -444,19 +444,18 @@ exports[`Home Page has no unexpected changes 1`] = `
       className="c7"
     >
       <a
-        className="c9"
-        href="https://gnomad.broadinstitute.org/short-tandem-repeats?dataset=gnomad_r3"
-        rel="noopener noreferrer"
-        target="_blank"
+        className="-Link c8"
+        href="/short-tandem-repeats?dataset=gnomad_r4"
+        onClick={[Function]}
       >
         Short tandem repeat
+         
       </a>
-       
       locus:
        
       <a
         className="-Link c8"
-        href="short-tandem-repeat/ATXN1?dataset=gnomad_r3"
+        href="short-tandem-repeat/ATXN1?dataset=gnomad_r4"
         onClick={[Function]}
       >
         ATXN1

diff --git a/dataset-metadata/metadata.ts b/dataset-metadata/metadata.ts
@@ -207,9 +207,9 @@ const metadataForDataset = (datasetId: DatasetId): DatasetMetadata => ({
   transcriptsHaveExomeCoverage: !datasetId.startsWith('gnomad_r3') && datasetId !== 'gnomad_sv_r4',
   referenceGenome:
     datasetId.startsWith('gnomad_r3') ||
-    datasetId.startsWith('gnomad_r4') ||
-    datasetId === 'gnomad_sv_r4' ||
-    datasetId === 'gnomad_cnv_r4'
+      datasetId.startsWith('gnomad_r4') ||
+      datasetId === 'gnomad_sv_r4' ||
+      datasetId === 'gnomad_cnv_r4'
       ? 'GRCh38'
       : 'GRCh37',
   genesHaveGenomeCoverage: !datasetId.startsWith('gnomad_cnv'),
@@ -245,7 +245,7 @@ const metadataForDataset = (datasetId: DatasetId): DatasetMetadata => ({
   hasRelatedVariants: datasetId !== 'gnomad_r2_1',
   showAllIndividualsInAgeDistributionByDefault: datasetId !== 'exac',
   hasExons: !datasetId.startsWith('gnomad_sv'),
-  hasShortTandemRepeats: datasetId.startsWith('gnomad_r3') || datasetId === 'gnomad_sv_r4',
+  hasShortTandemRepeats: datasetId.startsWith('gnomad_r3') || datasetId.startsWith('gnomad_r4') || datasetId === "gnomad_sv_r4",
   hasMitochondrialGenomeCoverage: !(datasetId === 'exac' || datasetId.startsWith('gnomad_r2')),
   hasMitochondrialVariants: !(datasetId === 'exac' || datasetId.startsWith('gnomad_r2')),
   hasNonCodingReadData: !(datasetId === 'exac' || datasetId.startsWith('gnomad_r2')),

diff --git a/graphql-api/src/queries/short-tandem-repeat-queries.ts b/graphql-api/src/queries/short-tandem-repeat-queries.ts
@@ -5,6 +5,7 @@ import { fetchAllSearchResults } from './helpers/elasticsearch-helpers'
 
 const SHORT_TANDEM_REPEAT_INDICES = {
   gnomad_r3: 'gnomad_v3_short_tandem_repeats',
+  gnomad_r4: 'gnomad_v3_short_tandem_repeats',
 }
 
 const SUMMARY_FIELDS = [